Transcription Initiation Defines Kinetoplast RNA Boundaries
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Transcription initiation defines kinetoplast RNA boundaries François M. Sementa,1, Takuma Suematsua,1, Liye Zhangb, Tian Yua,c, Lan Huangd, Inna Aphasizhevaa, and Ruslan Aphasizheva,e,2 aDepartment of Molecular and Cell Biology, Boston University, Boston, MA 02118; bSchool of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China; cBioinformatics Program, Boston University, Boston, MA 02215; dDepartment of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA 92697; and eDepartment of Biochemistry, Boston University, Boston, MA 02118 Edited by Brenda L. Bass, University of Utah School of Medicine, Salt Lake City, UT, and approved September 26, 2018 (received for review May 24, 2018) Mitochondrial genomes are often transcribed into polycistronic RNAs by 3′–5′ exonucleolytic trimming (13, 14). This reaction is carried punctuated by tRNAs whose excision defines mature RNA boundaries. out by DSS1 3′–5′ exonuclease (15) acting as a subunit of the Although kinetoplast DNA lacks tRNA genes, it is commonly held that mitochondrial 3′ processome (MPsome) (13). Recently, we in Trypanosoma brucei the monophosphorylated 5′ ends of func- established that rRNA and mRNA precursors accumulate upon ’ ′– ′ tional molecules typify precursor partitioning by an unknown knockdown of the MPsome s components (16). Hence, 3 5 endonuclease. On the contrary, we demonstrate that individual trimming appears to be the major, if not the only, nucleolytic mRNAs and rRNAs are independently synthesized as 3′-extended processing pathway. This modus operandi, however, would be ′ incongruent with a polycistronic precursor containing several precursors. The transcription-defined 5 terminus is converted in- ′ to a monophosphorylated state by the pyrophosphohydrolase coding sequences: Only the 5 region can be converted into pre- mRNA that is competent for polyadenylation and editing. Fur- complex, termed the “PPsome.” Composed of the MERS1 NUDIX en- thermore, any conceivable mechanism ought to account for the zyme, the MERS2 pentatricopeptide repeat RNA-binding subunit, and monophosphorylated 5′ termini and homogenous 3′ ends. MERS3 polypeptide, the PPsome binds to specific sequences near ′ ′ In this work, we demonstrate that mRNA and rRNA 5 ends mRNA 5 termini. Most guide RNAs lack PPsome-recognition sites are defined by transcription initiation, while the 3′-extended and remain triphosphorylated. The RNA-editing substrate-binding primary transcripts encroach into downstream genes. We pro- complex stimulates MERS1 pyrophosphohydrolase activity and en- vide several lines of evidence that triphosphate is most likely ables an interaction between the PPsome and the polyadenylation converted into monophosphate by MERS1 NUDIX [for “nu- machinery. We provide evidence that both 5′ pyrophosphate removal cleoside diphosphates linked to any moiety (x)”] hydrolase (17). and 3′ adenylation are essential for mRNA stabilization. Furthermore, Along with a MERS2 pentatricopeptide repeat (PPR) RNA- we uncover a mechanism by which antisense RNA-controlled 3′–5′ binding factor and a MERS3 subunit lacking any motifs, MERS1 exonucleolytic trimming defines the mRNA 3′ end before adenylation. constitutes a 5′ pyrophosphohydrolase complex, the PPsome. We conclude that mitochondrial mRNAs and rRNAs are transcribed This particle targets mRNA 5′ termini in vivo and displays an in and processed as insulated units irrespective of their genomic location. vitro hydrolase activity which is stimulated by the RNA-editing Trypanosoma | mitochondria | transcription | RNA stability | Significance NUDIX hydrolase It is held that in trypanosomes both mitochondrial DNA strands otwithstanding their monophyletic origin, present-day mi- are transcribed into polycistronic precursors. An unknown en- Ntochondria display an inexplicable diversity of transcrip- donuclease presumably cleaves primary transcripts to liberate tional, RNA processing, and translation mechanisms. In animals monocistronic mRNAs. However, this model is incongruent and fungi, mitochondrial DNA is transcribed into polycistronic with an established event of mRNA processing by 3′–5′ exo- primary RNAs, which are cleaved internally (1, 2), while in plants nucleolytic degradation. Our work suggests that each gene is diverse cis elements recruit RNA polymerases to individual genes transcribed individually and the pre-mRNA undergoes 5′-end (3). As suggested by the “tRNA punctuation” model, pre-mRNAs modification and controlled 3′-end trimming. We identified are liberated from polycistronic precursors via excision of flanking the pyrophosphohydrolase protein complex as responsible for tRNAs by RNases P and Z (4, 5). The causative agent of African pyrophosphate removal from the 5′ nucleoside and mRNA sleeping sickness, Trypanosoma brucei, maintains a bipartite mi- stabilization. We characterized antisense noncoding RNAs origi- tochondrial genome composed of a few ∼23-kb maxicircles and nating near mRNA 3′ termini and investigated their potential ′ BIOCHEMISTRY thousands of ∼1-kb minicircles. Maxicircles encode 9S and 12S role in 3 -end demarcation. It is conceivable that transcription, in rRNAs, 18 tightly packed protein genes, a single trans-acting addition to mRNA editing and decay, plays a significant role in MURF2-II guide RNA (gRNA), and a cis-acting gRNA embed- regulation of mitochondrial gene expression. ded into the 3′ UTR of CO2 mRNA. Minicircles produce most Author contributions: R.A. designed research; F.M.S., T.S., L.H., I.A., and R.A. performed gRNAs required for U-insertion/deletion mRNA editing (6). In- research; F.M.S., T.S., L.Z., T.Y., I.A., and R.A. analyzed data; and F.M.S. and R.A. wrote terestingly, mature rRNA and mRNA 5′ termini are mono- the paper. phosphorylated, while gRNAs retain triphosphate characteristic of The authors declare no conflict of interest. the transcription start site (7). A putative maxicircle transcription- This article is a PNAS Direct Submission. ∼ initiation region has been mapped to the major strand 1,200 nt Published under the PNAS license. upstream of the 12S rRNA, and the transcription is believed to Data deposition: The RNA-sequencing and KAP-sequencing data files have been depos- proceed polycistronically (8, 9). Although the absence of mito- ited in the BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) (accession no. chondrial tRNA genes (10) negates the tRNA punctuation sce- BioProject PRJNA402081). nario, it is commonly held that an unknown endonuclease cuts 1F.M.S. and T.S. contributed equally to this work. between functional sequences to liberate rRNAs and mono- 2To whom correspondence should be addressed. Email: [email protected]. cistronic pre-mRNAs (11, 12). This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. In contrast to maxicircle transcripts, gRNAs are synthesized 1073/pnas.1808981115/-/DCSupplemental. from dedicated promoters as ∼1-kb precursors and are processed Published online October 17, 2018. www.pnas.org/cgi/doi/10.1073/pnas.1808981115 PNAS | vol. 115 | no. 44 | E10323–E10332 Downloaded by guest on September 24, 2021 substrate-binding complex (RESC) (18). The PPsome apparently functions as a “protein cap” to stabilize monophosphorylated mRNAs by interacting with the kinetoplast polyadenylation complex (KPAC) to tether 5′ and 3′ termini. Finally, we propose a mechanism by which the antisense noncoding RNAs (ncRNAs) may modulate the 3′–5′ deg- radation activity of the mitochondrial MPsome (13), thereby defining the 3′ ends of maxicircle-encoded mRNAs. Results Kinetoplast Genes Are Transcribed as Independent Units. To in- vestigate mitochondrial RNA polymerase (MTRNAP) occupancy of the maxicircle DNA, we developed the kinetoplast affinity purification-sequencing (KAP-seq) protocol. The C-terminally tan- dem affinity purification (TAP)-tagged MTRNAP was expressed in an insect (procyclic) developmental form of the parasite and was verified to have been targeted to the mitochondrial matrix without appreciably impacting cell growth (SI Appendix,Fig.S1A and B). The 170-kDa MTRNAP-TAP protein was incorporated into an ∼900-kDa complex (Fig. 1A) which was resistant to RNase and DNase treatment (SI Appendix,Fig.S1C). Live cells were cross- linked with formaldehyde (Fig. 1B), and DNA was fragmented by focusedsonication(SI Appendix,Fig.S1D). At the ∼100-bp resolu- tion achieved with nonstranded KAP-seq (Fig. 1C), MTRNAP binding was detected predominantly within the conserved gene- containing region (Fig. 1D). This trend is particularly instructive for adjacent genes, such as 9S and 12S mitochondrial rRNAs or the ND7-CO3-cyb-A6 segment. Here, polycistronic transcription would be expected to correlate with uniform MTRNAP progression. However, the cyb gene clearly shows a decreased number of KAP- seq reads compared with neighboring ND7, CO3,andA6.Inthe segment devoid of annotated genes, a major occupancy peak matched the position of a previously mapped precursor of unknown function originating ∼1,200 nt upstream of the 12S rRNA (8). Al- though KAP-seq results do not entirely negate the polycistronic transcription model, the MTRNAP occupancy appears to correlate Fig. 1. RNA polymerase occupancy conforms to individual gene boundaries. with the positioning of individual rRNA and protein genes and with (A) Glycerol gradient fractionation of the MTRNAP complex. Mitochondrial ly- transcripts of unknown function. sate from cells expressing TAP-tagged MTRNAP was separated in a 10–30% glycerol gradient.